I am having the same experience as Vroni. This happens when I close the window by clicking the red button in upper left corner. Also when I use File > Close or Shift-Command-W.
It happens on multiple epubs and also on a blank epub (i.e., if I open new blank epub and save the initial blank file (Section0001.xhtml).
The only way to resolve this is to Quit Sigil altogether with Command-Q or menu equivalent.
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